World Health Organisation (WHO) describes tobacco as a killer of up to half of its users, and causes the death of no less than Six (6) million people yearly. Notwithstanding the notable achievement of public health policies in plummeting cigarette smoking in many countries, waterpipe smoking has sustained tobacco consumption even in the wake of these numerous stern tobacco control policies and regulations that are habitually cigarette-oriented. Hence, this study sought to determine the prevalence, harm perception and correlates of favourable harm perception of this emerging method of tobacco consumption among undergraduate students in University of Ibadan. A cross sectional descriptive study was conducted among 390 undergraduate students residing in the halls at the University of Ibadan. Data were obtained using a semi-structured questionnaire and analysed with SPSS 21. A Likert scale was used to determine the harm perception of waterpipe tobacco smoking by current smokers while Bi-variate analysis was used to test for associations and correlates of favourable harm perception. The study revealed that mean age of initiation of WPS was 18.5 ± 2.7years, 7.8% were ever users while 3.9% were current users with an intermittent pattern of use. 33% of current waterpipe users had favourable harm perception while 67% of them had unfavourable harm perception. Health warnings on shisha smoking packages and considering of shisha use as smoking were significant correlates of favourable harm perception while Shisha smoking among siblings of respondents, knowledge of waterpipe (Shisha) instrument, sex, current cigarette smoking status, and shisha smokers among friends were not significant. WPS is practiced among the University’s undergraduate students with less awareness on its health consequences. Hence, education and promotion of the intending harm in smoking waterpipe should be well advocated while specific laws should be formulated in the Tobacco Control Act to regulate its use in the country.